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Crystal Structure of PPARgamma Ligand Binding Domain in complex with dibenzooxepine derivative compound-17
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.05M Magnesium acetate, 0.1M Sodium acetate, 12% PEG 8,000
Crystal Properties Matthews coefficient Solvent content 2.4 48.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.34 α = 94.26 b = 54.06 β = 103.94 c = 70.49 γ = 89.95
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2010-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.84 43.96 95.8 0.101 5.3 1.9 52839
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.84 1.94 95 0.79 1.1 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.84 40 50181 2650 95.83 0.1947 0.19212 0.1994 0.24425 0.2481 RANDOM 36.27
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.49 0.02 0.84 -0.75 -0.25 0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.074 r_dihedral_angle_4_deg 17.645 r_dihedral_angle_3_deg 17.266 r_dihedral_angle_1_deg 5.978 r_long_range_B_refined 5.597 r_long_range_B_other 5.467 r_scangle_other 1.845 r_mcangle_it 1.822 r_mcangle_other 1.822 r_angle_refined_deg 1.582
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.074 r_dihedral_angle_4_deg 17.645 r_dihedral_angle_3_deg 17.266 r_dihedral_angle_1_deg 5.978 r_long_range_B_refined 5.597 r_long_range_B_other 5.467 r_scangle_other 1.845 r_mcangle_it 1.822 r_mcangle_other 1.822 r_angle_refined_deg 1.582 r_angle_other_deg 1.323 r_scbond_it 1.099 r_scbond_other 1.098 r_mcbond_it 1.05 r_mcbond_other 1.05 r_chiral_restr 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4419 Nucleic Acid Atoms Solvent Atoms 449 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing